How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it KNF Laboport series laboratory vacuum pump by 
Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01 How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Marshal Scientific MJ Research PTC-200 Thermal Cycler by Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01 How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Filtration with vacuum pump by Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01The first thing we did was to filter the water samples with a membrane filter that is so fine that not even bacteria can pass through, but water can.
Therefore, after filtration, we would have all particles such as bacteria and larger dirt pieces in the filter.
From the 1 liter in each bottle, we only used 400 ml because previous experiments showed that filtering the remaining 600 ml is very time consuming because the membrane filter gets clogged up.
Therefore, the filtration step allows us to reduce those 400 ml volumes to more manageable Eppendorf tube volumes: Figure 1. "An Eppendorf tube". Reagents are expensive, and lab bench centrifuges are small!
Labelled Eppendorf tubes on a rack
. Source. Since the filter is so fine, filtering by gravity alone would take forever, and so we used a vacuum pump to speed thing up!
For that we used:
Peeling the vacuum pump filter protection peel before usage
. Source. 
Placing the vacuum pump filter
. Source. arstechnica.com/information-technology/2016/11/private-microwave-networks-financial-hft/ The secret world of microwave networks (2016) Fantastic article.
Example:
- the three most table polymorphs of calcium carbonate polymorphs are:
Last updated 2018 as of 2021, but still just worked.
Gotta run github.com/feathersjs/feathers-chat first: github.com/feathersjs-ecosystem/feathers-chat-react/issues/5, then it worked:and on the other terminal:then visit localhost:3000/ and you can create an account and login, tested on Ubuntu 20.10. Data is stored on persistently.
git clone https://github.com/feathersjs/feathers-chat
cd feathers-chat
git checkout fd729a47c57f9e6170cc1fa23cee0c84a004feb5
npm install
npm startgit clone https://github.com/feathersjs-ecosystem/feathers-chat-react
cd feathers-chat-react
git checkout 36d56cbe80bbd5596f6a108b1de9db343b33dac3
npm install
npm startIf you disable JavaScript on Chromium, it stops working completely. There is a section on how to solve that at: docs.feathersjs.com/cookbook/express/view-engine.html but it does not cover React specifically. Codaisseur/feathersjs-react-redux-ssr might be good to look into.
Allow us to determine with good approximation in a multi-electron atom which electron configuration have more energy. It is a bit like the Aufbau principle, but at a finer resolution.
Note that this is not trivial since there is no explicit solution to the Schrödinger equation for multi-electron atoms like there is for hydrogen.
For example, consider carbon which has electron configuration 1s2 2s2 2p2.
gothinkster/node-express-realworld-example-app by Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01Good overgrown section in the middle of Fresnel's biography: en.wikipedia.org/w/index.php?title=Augustin-Jean_Fresnel&oldid=1064236740#Historical_context:_From_Newton_to_Biot.
Particularly cool is to see how Fresnel fully understood that light is somehow polarized, even though he did not know that it was made out of electromagnetism, clear indication of which only came with the Faraday effect in 1845.
spie.org/publications/fg05_p03_maluss_law:
At the beginning of the nineteenth century the only known way to generate polarized light was with a calcite crystal. In 1808, using a calcite crystal, Malus discovered that natural incident light became polarized when it was reflected by a glass surface, and that the light reflected close to an angle of incidence of 57° could be extinguished when viewed through the crystal. He then proposed that natural light consisted of the s- and p-polarizations, which were perpendicular to each other.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Sample collection by Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01As you would expect, not much secret here, we just dumped a 1 liter glass bottle with a rope attached around the neck in a few different locations of the river, and pulled it out with the rope.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Conclusions by Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-01 +Created 1970-01-01- against all odds, the experiment worked and we got DNA out of the water, despite a bunch of non-bio newbs actively messing with random parts of the experiment
- PuntSeq and Biomakespace people, and all those tho do scientific outreach, are awesome!
- biology is hard
- creating insanely media rich articles like this is also hard, but the following helped enormously:
- Wikimedia Commons to store large media files out of Git
- Asciidoctor extensions to easily include those media files. The lessons learnt in this article were then an important motivation for Ciro's OurBigBook Markup, to which this article was later migrated.
- Nomacs to give Google Photos photos meaningful names and to edit people's faces out of pictures ;-)
- some scientific Wikipedia pages may or may not have been edited with better pictures during the course of writing this article
Isomers were quite confusing for early chemists, before atomic theory was widely accepted, and people where thinking mostly in terms of proportions of equations, related: Section "Isomers suggest that atoms exist".
Fabry Perot Interferometer by JFC UCL (2016)
Source. Description only, reasonable animations. Considers the case of two nearby beam splitters.Fabry-Perot Introduction by Williams College Physics (2020)
Source. Shows a working device. Confocal optical cavity, one of the mirrors scans back and forward moved by a piezoelectric motor, this is called a "scanning Fabry-Perot interferometer".
Does not produce an interference pattern, only an on/off blob, which is then fed into an oscilloscope for analysis. The oscilloscope shows both the mirror displacement (which is given by a voltage) and the light detector output.
There are unlisted articles, also show them or only show them.